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- PDB-4uon: Crystal structure of C-terminal truncated (110-265) Aura virus ca... -

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Basic information

Entry
Database: PDB / ID: 4uon
TitleCrystal structure of C-terminal truncated (110-265) Aura virus capsid protease.
ComponentsCAPSID PROTEASE
KeywordsHYDROLASE
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesAURA VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsAggarwal, M. / Kumar, P. / Tomar, S.
CitationJournal: J.Virol. / Year: 2014
Title: Trans-Protease Activity and Structural Insights Into the Active Form of the Alphavirus Capsid Protease.
Authors: Aggarwal, M. / Dhindwal, S. / Kumar, P. / Kuhn, R.J. / Tomar, S.
History
DepositionJun 5, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionJun 18, 2014ID: 4AUS
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAPSID PROTEASE
B: CAPSID PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4778
Polymers33,9252
Non-polymers5536
Water7,206400
1
A: CAPSID PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2394
Polymers16,9621
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CAPSID PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2394
Polymers16,9621
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.560, 71.350, 61.510
Angle α, β, γ (deg.)90.00, 114.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CAPSID PROTEASE / P130 / COAT PROTEIN / C / E3/E2 / SPIKE GLYCOPROTEIN E3 / SPIKE GLYCOPROTEIN E2 / SPIKE GLYCOPROTEIN E1


Mass: 16962.266 Da / Num. of mol.: 2 / Fragment: RESIDUES 110-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AURA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q86925, togavirin
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSOME RESIDUES ARE DIFFERENT IN OUR SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.97 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM CITRATE TRIBASIC DIHYDRATE & 20% W/V POLYETHYLENE GLYCOL 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 3, 2011 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→56.07 Å / Num. obs: 38673 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.1
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3 / % possible all: 83.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AGK
Resolution: 1.81→56.08 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.461 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 262-265 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21855 1934 5 %RANDOM
Rwork0.18284 ---
obs0.18464 36720 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.006 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å2-0.12 Å2
2---0.37 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.81→56.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 36 400 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222443
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9523298
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2265321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.7723.87193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44415402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.155158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211826
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7791.51539
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42522461
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3723904
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8534.5831
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.805→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 130 -
Rwork0.373 2554 -
obs--93.19 %

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